Just seeing this thread for the first time, but I had terrible knee pain the first week of cycling and it turned out to be the seat was too low and also too far back. Seat placement is really simple if you're a professional, so I'm surprised your LBS didn't get it right the first time! I bought my bike over the internet, so had to figure out all the fitting stuff myself through trial and error and lots of internet info.

Hope the pain doesn't return for you!